Q3ta options

[holmeso]

Description

Added a Main class whose sole purpose is to give the general usage instructions for the q3tiledaligner project. Updated usage for the GenerateTiledAligerFile class.

fixes #306

Type of change

Please delete options that are not relevant.

• [X] Bug fix (non-breaking change which fixes an issue)
• [X] This change requires a documentation update

How Has This Been Tested?

Existing unit tests pass

Are WDL Updates Required?

No wdl updates required

Checklist:

• [X] My code follows the style guidelines of this project
• [X] I have performed a self-review of my own code
• [X] I have commented my code, particularly in hard-to-understand areas
• [X] I have made corresponding changes to the documentation
• [X] My changes generate no new warnings
• [X] New and existing unit tests pass locally with my changes

[holmeso]

Point taken. I can't find a way for OptionParser to only take a subset of the options when displaying the help so I have removed the calls to displayHelp as suggested.